Haplotype inferring via galled-tree networks using a hypergraph covering problem for special genotype matrices

Authors:
Arvind Gupta;Ján Maňuch;Ladislav Stacho;Xiaohong Zhao
Affiliations:
School of Computing Science and Department of Mathematics, Simon Fraser University, Canada;School of Computing Science and Department of Mathematics, Simon Fraser University, Canada;School of Computing Science and Department of Mathematics, Simon Fraser University, Canada;School of Computing Science and Department of Mathematics, Simon Fraser University, Canada
Venue:
Discrete Applied Mathematics
Year:
2009

Citing 7
Cited 3

Haplotyping as perfect phylogeny: conceptual framework and efficient solutions

Proceedings of the sixth annual international conference on Computational biology
Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination

CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Optimal, efficient reconstruction of root-unknown phylogenetic networks with constrained and structured recombination

Journal of Computer and System Sciences - Special issue on bioinformatics II
A Concise Necessary and Sufficient Condition for the Existence of a Galled-Tree

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Haplotype inference by pure Parsimony

CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Algorithm for haplotype inferring via galled-tree networks with simple galls

ISBRA'07 Proceedings of the 3rd international conference on Bioinformatics research and applications
Algorithms for imperfect phylogeny haplotyping (IPPH) with a single homoplasy or recombination event

WABI'05 Proceedings of the 5th International conference on Algorithms in Bioinformatics

Haplotype Inferring Via Galled-Tree Networks Is NP-Complete

COCOON '08 Proceedings of the 14th annual international conference on Computing and Combinatorics
The complexity of the gapped consecutive-ones property problem for matrices of bounded maximum degree

RECOMB-CG'10 Proceedings of the 2010 international conference on Comparative genomics
Phylogeny- and parsimony-based haplotype inference with constraints

Information and Computation

Quantified Score

Hi-index	0.04

Visualization

Abstract

Since exact determination of haplotype blocks is usually not possible, it is desirable to develop a haplotyping method which can account for recombinations. A natural candidate for such a method is haplotyping via phylogenetic networks or their simplified version: galled-tree networks. In earlier work we characterized the existence of the galled-tree networks. Building on this, we reduce the problem of haplotype inferring via galled-tree networks to a hypergraph covering problem for genotype matrices satisfying a combinatorial condition. Our experiments on actual data show that this condition is almost always satisfied when the percentage of minor alleles for each SNP reaches at least 30%.